Functional Enrichment Analysis | Tool: gprofileR.

net_dir = "/pastel/projects/speakeasy_dlpfc/SpeakEasy_singlenuclei/2nd_pass/snakemake-sn/results/"

macro_type = params$cell_type #macro_structure. It can be cell_type, metabolites, region of the brain. 
message(paste0("Cluster: ", macro_type))
## Cluster: inh

Enrichment Level 03

We removed the clusters with < 30 nodes for downstream analysis.

modules_file = read.table(paste0(net_dir, macro_type, "/geneBycluster.txt"), header = T)
modules_file = modules_file[, c("gene_name", "cluster_lv3")]
modules_file$module_clusters = paste0("m", modules_file$cluster_lv3)
modules_file$cluster_lv3 = NULL
colnames(modules_file) = c("symbol", "module_clusters") #only the sn was with gene_name instead of symbol

modules_size = as.data.frame(table(modules_file$module_clusters))
colnames(modules_size) = c("module", "n_nodes")
createDT(modules_size)

Module enrichment L3

Module m20

Module m1

Module m27

Module m31

Module m2

Module m29

Module m16

Module m15

Module m5

Module m18

Module m28

Module m19

Module m6

Module m4

Module m22

Module m3

Module m23

Module m30

Module m7

Module m24

Module m17

Module m32

Module m8

Session info

sessionInfo()

R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Stream 8

Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] DT_0.20 plotly_4.10.0 knitr_1.37 gprofiler2_0.2.1 ggeasy_0.1.3 readxl_1.3.1 kableExtra_1.3.4 R.matlab_3.6.2 forcats_0.5.1 stringr_1.4.0
[11] dplyr_1.0.8 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.6 tidyverse_1.3.1 limma_3.50.1 ggfortify_0.4.14 ggplot2_3.3.5

loaded via a namespace (and not attached): [1] bitops_1.0-7 fs_1.5.2 lubridate_1.8.0 webshot_0.5.2 RColorBrewer_1.1-2 httr_1.4.2 tools_4.1.2 backports_1.4.1 bslib_0.3.1
[10] utf8_1.2.2 R6_2.5.1 vipor_0.4.5 DBI_1.1.2 lazyeval_0.2.2 colorspace_2.0-3 withr_2.4.3 tidyselect_1.1.2 gridExtra_2.3
[19] compiler_4.1.2 cli_3.2.0 rvest_1.0.2 xml2_1.3.3 sass_0.4.0 scales_1.1.1 systemfonts_1.0.4 digest_0.6.29 rmarkdown_2.11
[28] svglite_2.1.0 R.utils_2.11.0 pkgconfig_2.0.3 htmltools_0.5.2 dbplyr_2.1.1 fastmap_1.1.0 htmlwidgets_1.5.4 rlang_1.0.1 rstudioapi_0.13
[37] shiny_1.7.1 jquerylib_0.1.4 generics_0.1.2 jsonlite_1.7.3 crosstalk_1.2.0 R.oo_1.24.0 RCurl_1.98-1.6 magrittr_2.0.2 Rcpp_1.0.8
[46] ggbeeswarm_0.6.0 munsell_0.5.0 fansi_1.0.2 lifecycle_1.0.1 R.methodsS3_1.8.1 stringi_1.7.6 yaml_2.3.5 grid_4.1.2 promises_1.2.0.1
[55] crayon_1.5.0 haven_2.4.3 hms_1.1.1 pillar_1.7.0 reprex_2.0.1 glue_1.6.1 evaluate_0.15 data.table_1.14.2 modelr_0.1.8
[64] httpuv_1.6.5 vctrs_0.3.8 tzdb_0.2.0 cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1 xfun_0.29 mime_0.12 xtable_1.8-4
[73] broom_0.7.12 later_1.3.0 viridisLite_0.4.0 pheatmap_1.0.12 beeswarm_0.4.0 ellipsis_0.3.2